Eisen Lab in the News

“This study reflects a growing trend of trying to connect the microbiomes on various plants and animals to the microbiomes of the human built environments in which these organisms reside,” says Jonathan Eisen, a biology professor at the University of California at Davis who was not involved in the new research. “We need to start to study this in more detail in order to better understand how to optimize the built environment to promote the health of residents—whether human, other animals, plant, or other.”

“At his blog, Jonathan Eisen has awarded his ‘Overselling the Microbiome’ award to the New York Times for its coverage of a study that found that kids who sucked their thumbs or bit their nails were less likely to develop allergies”

July 7, 2016. Ann Griswold in Spectrum. Single microbe may restore social behaviors in mice

The scientific community should “be very careful about how we present and interpret such work,” says Jonathan Eisen, professor of medical microbiology and immunology at the University of California, Davis. Eisen has been openly critical of the study’s media coverage.

Meanwhile, analyzing toilet waste for public health is an idea still just floating around. “I’m not surprised that microbes vary between samples and they are related to the country of origin,” says Jonathan Eisen, a microbiologist at the University of California, Davis. “It’s a nice concept, but I’m not overwhelmed by the implications yet.” If scientists could actually link DNA sequences to an outbreak, they’d be onto something. Fortunately, science is commodious when it comes to accepting new ideas. If researchers need to plumb their imaginations for a new approach, well, that’s almost interesting enough (in lieu of actual results). They’re just doing their duty.

I asked Jonathan Eisen, a microbiome expert at the University of California, Davis, about Brain Maker. “To think we can magically heal diseases by changing to a gluten-free diet and taking some probiotics is idiotic, quite frankly,” he told me. After Eisen read the case study of an autistic boy that Perlmutter highlights in Brain Maker and on his website — “from a scientific perspective, [fecal transplantation for autism] makes absolute sense” — his words were even harsher. “It resembles more the presentation of a snake-oil salesman than that of a person interested in actually figuring out how to help people,” said Eisen.

A new UC Davis study will analyze the bacteria in cats in the hopes of better understanding our pets and maybe ourselves. The “Kitty Biome Project” is directed by Jonathan Eisen. He’s a microbial ecology professor at UC Davis. He suspects people and their cats might have more in common than anyone knew.“[There are] hundreds of papers now where people have used the microbial community as a potential diagnostic for gut problems, for cancer, skin problems, behavior, for forensic purposes,” says Eisen. “And the same is true of cats if you want to understand what’s going in the health of your cat it’s really easy to collect a fecal sample from a kitty litter.”Eisen hopes to answer questions like: How do athletic cats compare to couch potato cats. Or, does it matter if you feed your cat a paleo-mouse diet? Or, what happens when your cat takes antibiotics?

But some researchers are now worried that these powerful drugs are wrecking koalas’ gut microbiotas—in particular the microbes that digest otherwise toxic eucalyptus leaves, koalas’ only food source. “Koalas represent a fascinating case study of a rare extreme in mammals—where we know specific functions of the microbiome that are required for survival,” says Jonathan Eisen, an evolutionary biologist at the University of California, Davis.

“Eisen called the Sonnenburg’s approach and that of Martin Blaser, an NYU microbiologist who wrote the book Missing Microbes, “reasonably responsible.” He does not feel the same about other books. “Most of them are ridiculous — just completely outlandish claims with no basis in science.”

“Eisen took particular exception to claims made by David Perlmutter, author of the microbiome book Brain Maker, calling them “at best horribly misleading.” Brain Maker uses much stronger language than the Sonnenburgs when it comes to the brain-gut link, an area of research that has implications for disorders such as autism; the diet Perlmutter recommends bans gluten and advises lighter legume consumption.”

“For instance, Jonathan Eisen, a professor of microbiology at the University of California at Davis, has tracked diversity in STEM fields for several years. His commentary on the issue includes a running list of conferences with poor gender ratios among speakers.”

Not surprisingly, many in the scientific community don’t agree with the authors’ conclusions. One criticism, voiced by the University of California, Davis’s Jonathan Eisen on his The Tree of Life blog, is that “career progression” topics—like salary and promotion—are lumped in with workplace topics—such as hostility and physical aggression against women—and yet, the authors only discuss data relevant to the career progression-related issues. Evidence suggesting relative equality in this area, then, seems to have led to the assumption that “other workplace issues must not be a problem,” Eisen wrote. “[That’s] a dangerous and unsupported connection.”

“In July, Jonathan Eisen—one of science’s most famous Twitter personalities and the author of the popular blog The Tree of Life—was lauded for turning down a paid honorarium at a conference because there were too few women invited to speak there. According to Eisen, there is no basis for an uneven ratio of male to female speakers in biology because there are enough women doing great work to be included equally alongside their male peers—in his letter to the conference host, he wrote, “As someone who is working actively on multiple issues relating to gender bias in science, I find this [gender ratio skew] very disappointing. … I simply cannot personally contribute to a series which has such an imbalance and I would suggest that you consider whether anything in your process is biased in some way.”

“CHEERS to Jonathan Eisen, a professor of microbiology at UC Davis, who recently turned down an opportunity to be part of a lecture series at another university on principle — too few women were invited. “In my field, there just isn’t that big of a difference in the percentage of males and females at various academic levels,” Eisen said. “And so when there’s a skewed ratio, there’s a sign that something is amiss.” Eisen said the response to his decision, which also included turning down a $2,000 honorarium, has been “amazingly positive.” Add our voice to the chorus: Thanks, Professor, for not just talking the talk, but for walking the walk.”

“Given the virus’s abundance and how widespread it is, it is probably going to be very important for understanding the ecology of the human gut,” University of California, Davis, microbiologist Jonathan Eisen, who was not involved in the study, told NPR. “And it likely infects a group of organisms [the Bacteroides] thought to be really important for health.”

“Over at his Tree of Life blog, Jonathan Eisen, a professor of evolution and ecology and medical microbiology at the University of California, Davis, remembered Riley as a “wonderful person,” he wrote. “Among her many achievements, she was central to the annotation of the E. coli genome and in keeping track of all the studies that had been done on various E. coli genes,” continued Eisen.”

October 9-15: Coverage of editorial by Eisen et al. on impact fact and peer review